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NBCC Open Notebook Science Talk

NBCC Open Notebook Science Talk



Jean-Claude Bradley presents "Accelerating Discovery by Sharing: a case for Open Notebook Science" at the National Breast Cancer Coalition Annual Advocacy Conference in Arlington, VA on May 1, ...

Jean-Claude Bradley presents "Accelerating Discovery by Sharing: a case for Open Notebook Science" at the National Breast Cancer Coalition Annual Advocacy Conference in Arlington, VA on May 1, 2011.



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    NBCC Open Notebook Science Talk NBCC Open Notebook Science Talk Presentation Transcript

    • Accelerating Discovery by Sharing: a case for Open Notebook Science Jean-Claude Bradley May 1, 2011 National Breast Cancer Coalition Annual Advocacy Conference Associate Professor of Chemistry Drexel University
    • Outline
      • Trends in sharing for drug discovery
      • ONS for malaria research
      • Crowdsourcing solubility with ONS
      • Leveraging the educational system to contribute new science
      • Open modeling and web services
      • Discovering connections
      • Moving forward: tools and practices
    • Industry is Sharing More
    • Opportunities for Competitive Collaboration
    • Some Initiatives Promoting More Openness in Drug Discovery
    • Motivation: Faster Science, Better Science
    • There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
    • First record then abstract structure In order to be discoverable use Google friendly formats (simple HTML, no login) In order to be replicable use free hosted tools (Wikispaces, Google Spreadsheets) Strategy for an Open Notebook:
    • UsefulChem Project: Open Primary Research in Drug Design using Web2.0 tools Docking Synthesis Testing Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang Inst.
    • Malaria Target: falcipain-2 involved in hemoglobin metabolism Dana.org
    • The Ugi Reaction
    • Outcome of Guha-Bradley-Rosenthal collaboration
    • References to papers, blog posts, lab notebook pages, raw data
    • The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?
    • Crowdsourcing Solubility Data
    • ONS Challenge Judges
    • ONS Challenge Award Winners
    • Solubilities collected in a Google Spreadsheet
    • Rajarshi Guha’s Live Web Query using Google Viz API
    • Data provenance: From Wikipedia to…
    • … the lab notebook and raw data
    • Interactive NMR spectra using JSpecView and JCAMP-DX
    • (Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)
    • Raw Data As Images Splatter? Some liquid
    • YouTube for demonstrating experimental set-up
    • The importance of raw data availability Missed in a prior publication on solubility for this compound
    • Case study: Chemical Information Retrieval course at Drexel (Fall 2009/2010) Leveraging the educational system to contribute new science
    • The Chemical Information Validation Sheet 567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course
    • The Chemical Information Validation Explorer (Andrew Lang)
    • Discovering outliers for melting points (stdev/average)
    • Investigating the m.p. inconsistencies of EGCG
    • Investigating the m.p. inconsistencies of cyclohexanone
    • Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for melting points
    • Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for boiling points
    • Sigma-Aldrich, Acros and Wolfram Alpha apparently DO NOT use the same sources for flash points
    • Most popular data sources
    • Alfa Aesar donates melting points to the public
    • Open Melting Point Explorer
    • Outliers MDPI dataset EPI (via ChemSpider)
    • Outliers Alfa Aesar
    • Inconsistencies and SMILES problems within MDPI dataset
    • MDPI Dataset labeled with High Trust Level
    • Open Melting Point Datasets
    • Open Random Forest modeling of Open Melting Point data using CDK descriptors (Andrew Lang) R2 = 0.78, TPSA and nHdon most important
    • Melting point prediction service
    • Other Web Services… (Andrew Lang) General Transparent Solubility Prediction
    • Convenient web services for solubility measurement and prediction (Andrew Lang)
    • Integration of Multiple Web Services to Recommend Solvents for Reactions (Andrew Lang)
    • Using melting point for temperature dependent solubility prediction
    • Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)
    • Solubility Prediction (Andy Lang uses Abraham Model)
    • Reaction Attempts Book
    • Reaction Attempts Book: Reactants listed Alphabetically
    • Dynamic links to private tagged Mendeley collections (Andrew Lang)
    • All ONS web services
    • For all Formats of ONS Projects
    • ONS Challenge Solubility Book cited for nanotechnology application
    • Visualizing molecule-researcher connection maps reveals link between 2 Open Notebooks (Todd and Bradley) (Don Pellegrino)
    • The Intersection of Open Notebooks (Bradley/Todd) and IP implications Open Notebook could have blocked patent if done earlier
    • Decanoic acid Water NaCl
    • Phrase searching for useful solubility applications
    • Search for applications of solubility for breast cancer research
    • Solubility prediction for Taxol using Abraham descriptors Pred Exp
    • Predicted temperature dependent solubility of Taxol in water (M)
    • Current research questions for Taxol solubility
      • Does Taxol have a meaningful solubility in methanol or does it decompose too quickly?
      • Why is methanol reported to decompose Taxol but not ethanol?
      • Can the solubility of Taxol in solvent mixtures be predicted, especially for approved excipients?
      • Can the solubility of Taxol analogs be used to create reliable models for the solubility of this class of compounds?
    • Moving Forward: Tools and Practices Use free hosted web tools and open data formats
      • Google Spreadsheets (numerical data)
      • Wikispaces (human readable format)
      • YouTube, SlideShare, LuLu, Nature Precedings, etc. (multiple data formats)
      • JCAMP-DX for spectral data
      • Report all findings immediately – even if tentative
      • Participate in social media to share progress and find collaborators
      • Abstract experiments and findings to machine readable formats and make these easily discoverable